Let’s work on your original first, Sidle. I would delete the:
Special emphasis should be given to the mistake commentation.
Now, the normal position for new or stressed information in an English sentence is at the end, where you originally have it.
Casting a statement into a cleft-sentence form is a popular grammar exercise in foreign language classes, but the result, as in your examples, is usually awkward and unnatural.
Given that both of your sentences #1 and #2 are odd in that form, the difference would be in the reader’s tolerance for the dangling preposition to. Many prescriptive grammarians would still insist on #1.
Not really. You say the relative pronoun form whom has lost currency but I wonder with whom? Not with me! It is still used in the stressed position after prepositions if for no other reason than that it is easier to say.